I started using CellProfiler a couple hours ago, and I could use some help with my first hamfisted attempt at making a pipeline.
I have time-lapse images of neurons stained with a calcium indicator, saved as .nd2 files (I can also do .tif files with frames if that works better). I would like to have a spreadsheet showing each cell’s intensity in each frame, so I can plot them and figure out how many calcium events each cell had during the imaging session.
There are some modules that are obviously related to what I need to do (IdentifyPrimaryObjects, MeasureObjectIntensity, ExportToSpreadsheet) but when I run the pipeline I made from them, it only seems to measure one frame of the image. I think it understands that the file is actually a stack, since I have the option to analyze as 2-D or 3-D and I can make a maximum intensity projection, but there’s only one frame’s worth of data in the output spreadsheet. How can I get it to do all of the frames?
I’m sure this must have been asked before, but when I search I’m mainly turning up questions about processing movies where each frame is a separate file.
test.cpproj (417.1 KB)
Results_Cells.csv (153.9 KB)
(Edit: it looks like my tiff file is too big to attach–let me know if it would help to provide a more detailed description or a couple example frames)